In this markdown I would like to run my newts and snake simulation on a larger map. The prediction that is when I create a larger map there will be more opportunities for different areas to co-evolve, creating a mosaic pattern. The BIG map to be 100 times larger than the long map. The demotions would be; length=1,400 width=350. This would increase the amount of individuals and grid data-points in my simulations.

In my current simulations, there are about 6,000 individuals (combination of newts and snakes). If I increase the map’s area by 100 I expect that the number of individuals would also increase by 100 (~600,000). To make these simulations work/run faster I will increase the starting population size to 2,500 per each species. I also plan on taking information from the simulations less often (e.g. taking information every 50 generations instead of 20) and for a shorter amount of time (e.g. from 50,000 generation to only 10,000 generations).

My previous simulations ran for 50,000 generations and took a day or less to run (msprime+slim). I will make some plots to see how long these larger simulations will take to run

## All cor, lit, and grid files exist!
## This program will now end!

Phenotype differences

##                 Group.1          x
## 1 1e-09_0.05_1e-09_0.05  0.5168421
## 2  1e-09_0.05_1e-10_0.5 -2.0282711
## 3    1e-09_0.05_1e-11_5  0.4491350
## 4  1e-10_0.5_1e-09_0.05 -1.5476608
## 5   1e-10_0.5_1e-10_0.5 -2.1132919
## 6     1e-10_0.5_1e-11_5  1.7562747
## 7    1e-11_5_1e-09_0.05 -1.9341712
## 8     1e-11_5_1e-10_0.5 -2.0895114
## 9       1e-11_5_1e-11_5  0.3702103

Connection between higher phenotype and population (5 sec)

Phenotype differences

Phenotype & Populationsize differences

correlation

Correlation across time

Next, we will examine three randomly chosen plots from both the 5 section and 7 section experiment. Time (in generations) in on the x-axis and both mean phenotype and phenotype spatial correlation in on the y-axis. Newt whole population mean phenotype is red, while snake mean phenotype is blue. The pink line is the phenotype spatial correlation.

Random 1

Random 2

Random 3

Summary

In the summary section, I try to come up with a way to show how different GA combinations can change the simulations results. In all of these plots snakes GA is represented by color and newt GA is represented by shape. There 16 color-shape combinations (with 4 repeats for trials). There are four sets of plots: 1) newt by snake population size, 2) phenotype difference by snake population size, 3) phenotype difference by snake GA, and 4) phenotype difference by newt GA. There are three figures in each set, taken at the begging, middle, and end time chunks. These are whole population calculations so the 5 section and 7 section data sets are not calculated differently.

Early-Sim Population Size Summary

Early Difference Summary

By Snake GA

By Newt GA

Heatmap

Population Size

Phenotype

What is up with the correlations

Mean

## [1] 0.03397084

## [1] -0.278669